Germanium is a promising high-mobility channel material for future nanoelectronic devices. Hydrogen silsesquioxane (HSQ) is a well known high-resolution electron beam lithography (EBL) resist, which is usually developed in aqueous based developers. However, this feature of HSQ causes troubles while patterning Ge surface as it is always shielded with native Ge oxides. GeO2 is a water soluble oxide, and since HSQ resist is developed in aqueous solvents, this oxide interferes with the patterning. After the EBL exposure, GeO2 is washed off during the development, lifting the patterned structures and making the high-resolution patterning impossible. To avoid this issue, it is necessary to either clean and passivate the Ge surface or use buffer layers between the native Ge oxides and the HSQ layer. In this article, a novel technique to clean the Ge surface prior to HSQ deposition, using simple "household" acids like citric acid and acetic acid, is reported. The acids are able to remove the native Ge oxides as well as efficiently passivate the surface. The acid passivation was found to hold the HSQ sturdily to the Ge surface, even during development with the aqueous salty solvent. Using this process, Ge nanowires having widths down to 5 nm were successfully patterned on germanium-on-insulator substrates. To the best of our knowledge, these are the smallest top-down fabricated Ge nanostructures reported till date. (C) 2016 American Vacuum Society.